Pau Badia-i-Mompel
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: RELEASE_3_22 |
| git_last_commit: ff3aa1d |
| git_last_commit_date: 2025-10-29 11:09:41 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 541/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.16.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz |
| StartedAt: 2025-11-14 22:55:33 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 23:32:38 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 2225.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2025-11-14 22:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 22:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 22:56:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-14 22:56:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-14 22:56:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-14 22:56:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-14 22:56:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-14 22:56:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-14 22:56:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-14 22:56:08] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-14); AnnotationDbi 1.72.0(2025-11-14); AUCell 1.32.0(2025-11-14); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-14); Biobase 2.70.0(2025-11-14); BiocGenerics 0.56.0(2025-11-14); BiocParallel 1.44.0(2025-11-14); BiocSingular 1.26.0(2025-11-14); Biostrings 2.78.0(2025-11-14); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-14); DelayedArray 0.36.0(2025-11-14); DelayedMatrixStats 1.32.0(2025-11-14); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-14); GSEABase 1.72.0(2025-11-14); GSVA 2.4.1(2025-11-14); h5mread 1.2.0(2025-11-14); HDF5Array 1.38.0(2025-11-14); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-14); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-14); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-14); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.18.1(2025-11-14); otel 0.2.0(2025-08-29); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-14); rhdf5filters 1.22.0(2025-11-14); Rhdf5lib 1.32.0(2025-11-14); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-14); S4Vectors 0.48.0(2025-11-14); ScaledMatrix 1.18.0(2025-11-14); Seqinfo 1.0.0(2025-11-14); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-14); SparseArray 1.10.1(2025-11-14); sparseMatrixStats 1.22.0(2025-11-14); SpatialExperiment 1.20.0(2025-11-14); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-14 22:56:08] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Contains 10 files.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-14 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-14 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-14 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-14 22:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 22:56:08] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_collectri 31.710 2.440 294.842
get_dorothea 22.006 0.794 26.110
run_fgsea 21.614 0.527 22.148
run_aucell 8.894 1.602 10.523
get_progeny 6.144 0.363 14.425
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 23:03:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-14 23:03:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-14 23:03:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-14 23:03:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-14 23:03:55] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-14 23:03:55] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-14 23:03:55] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-14 23:03:55] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-14); AnnotationDbi 1.72.0(2025-11-14); AUCell 1.32.0(2025-11-14); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-14); Biobase 2.70.0(2025-11-14); BiocGenerics 0.56.0(2025-11-14); BiocParallel 1.44.0(2025-11-14); BiocSingular 1.26.0(2025-11-14); Biostrings 2.78.0(2025-11-14); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-14); DelayedArray 0.36.0(2025-11-14); DelayedMatrixStats 1.32.0(2025-11-14); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-14); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-14); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-14); GSEABase 1.72.0(2025-11-14); GSVA 2.4.1(2025-11-14); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-14); HDF5Array 1.38.0(2025-11-14); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-14); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-14); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-14); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.1(2025-11-14); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-14); rhdf5filters 1.22.0(2025-11-14); Rhdf5lib 1.32.0(2025-11-14); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-14); S4Vectors 0.48.0(2025-11-14); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-14); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.0.0(2025-11-14); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-14); SparseArray 1.10.1(2025-11-14); sparseMatrixStats 1.22.0(2025-11-14); SpatialExperiment 1.20.0(2025-11-14); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-14); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-14); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-14 23:03:55] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Contains 10 files.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-14 23:03:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-11-14 23:03:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:03:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:03:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:03:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:58] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:03:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:03:58] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-14 23:03:58] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-14 23:03:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:03:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:03:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:03:58] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-14 23:04:59] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-11-14 23:05:04] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-14 23:05:04] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-14 23:05:04] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:05:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:05:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:05:04] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:05:04] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-14 23:06:05] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-11-14 23:06:10] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-14 23:06:10] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-14 23:06:10] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:06:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:06:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:06:10] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:06:10] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-14 23:07:11] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-11-14 23:07:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-14 23:07:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-14 23:07:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-14 23:07:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-14 23:07:11] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-14 23:07:11] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-14 23:07:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-14 23:07:11] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-14); AnnotationDbi 1.72.0(2025-11-14); AUCell 1.32.0(2025-11-14); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-14); Biobase 2.70.0(2025-11-14); BiocGenerics 0.56.0(2025-11-14); BiocParallel 1.44.0(2025-11-14); BiocSingular 1.26.0(2025-11-14); Biostrings 2.78.0(2025-11-14); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-14); DelayedArray 0.36.0(2025-11-14); DelayedMatrixStats 1.32.0(2025-11-14); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-14); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-14); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-14); GSEABase 1.72.0(2025-11-14); GSVA 2.4.1(2025-11-14); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-14); HDF5Array 1.38.0(2025-11-14); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-14); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-14); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-14); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.1(2025-11-14); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-14); rhdf5filters 1.22.0(2025-11-14); Rhdf5lib 1.32.0(2025-11-14); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-14); S4Vectors 0.48.0(2025-11-14); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-14); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.0.0(2025-11-14); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-14); SparseArray 1.10.1(2025-11-14); sparseMatrixStats 1.22.0(2025-11-14); SpatialExperiment 1.20.0(2025-11-14); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-14); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-14); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-14 23:07:11] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-14 23:07:13] [ERROR] [OmnipathR] Failed to download Ensembl organisms table.
[2025-11-14 23:07:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-14 23:07:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-14 23:07:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-14 23:07:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-14 23:07:13] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-14 23:07:14] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-14 23:07:14] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-14 23:07:14] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-14); AnnotationDbi 1.72.0(2025-11-14); AUCell 1.32.0(2025-11-14); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-14); Biobase 2.70.0(2025-11-14); BiocGenerics 0.56.0(2025-11-14); BiocParallel 1.44.0(2025-11-14); BiocSingular 1.26.0(2025-11-14); Biostrings 2.78.0(2025-11-14); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-14); DelayedArray 0.36.0(2025-11-14); DelayedMatrixStats 1.32.0(2025-11-14); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-14); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-14); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-14); GSEABase 1.72.0(2025-11-14); GSVA 2.4.1(2025-11-14); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-14); HDF5Array 1.38.0(2025-11-14); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-14); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-14); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-14); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.1(2025-11-14); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-14); rhdf5filters 1.22.0(2025-11-14); Rhdf5lib 1.32.0(2025-11-14); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-14); S4Vectors 0.48.0(2025-11-14); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-14); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.0.0(2025-11-14); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-14); SparseArray 1.10.1(2025-11-14); sparseMatrixStats 1.22.0(2025-11-14); SpatialExperiment 1.20.0(2025-11-14); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-14); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-14); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-14 23:07:14] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:14] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:14] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-11-14 23:07:14] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-14 23:07:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:07:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:07:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-14 23:07:14] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-14 23:07:15] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-11-14 23:07:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:07:15] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.712085s from rescued.omnipathdb.org (56 Kb/s); Redirect: 0s, DNS look up: 0.008476s, Connection: 0.009771s, Pretransfer: 0.384207s, First byte at: 0.549572s
[2025-11-14 23:07:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:07:15 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 15 Nov 2025 05:07:15 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:07:15] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 15 Nov 2025 04:07:15 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 15 Nov 2025 05:07:15 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2025-11-14 23:07:16] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2025-11-14 23:07:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:16] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2025-11-14 23:07:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-14 23:07:17] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:17] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-14 23:07:17] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-14 23:07:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:07:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:07:17] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-14 23:07:17] [TRACE] [OmnipathR] Downloaded 11.2 Kb in 0.639999s from omabrowser.org (17.5 Kb/s); Redirect: 0s, DNS look up: 0.001787s, Connection: 0.002493s, Pretransfer: 0.450384s, First byte at: 0.639326s
[2025-11-14 23:07:17] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 15 Nov 2025 04:07:17 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-14 23:07:19] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-14 23:07:19] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:19] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-14 23:07:19] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-14 23:07:19] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-14 23:07:49] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:49] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-14 23:07:49] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:07:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:07:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:07:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:07:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:07:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:07:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.383724s from omnipathdb.org (40.8 Kb/s); Redirect: 0s, DNS look up: 0.001831s, Connection: 0.002636s, Pretransfer: 0.220522s, First byte at: 0.383313s
[2025-11-14 23:07:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:07:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:07:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:07:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-14 23:07:52] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:07:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-11-14 23:07:52] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-11-14 23:07:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:07:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:53] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:07:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-14 23:07:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:07:54] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:07:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:07:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:07:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:07:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:07:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:07:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:07:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:07:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.384128s from omnipathdb.org (40.8 Kb/s); Redirect: 0s, DNS look up: 0.001602s, Connection: 0.002291s, Pretransfer: 0.217942s, First byte at: 0.383738s
[2025-11-14 23:07:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:07:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:07:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:08:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:08:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:04] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:08:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-14 23:08:06] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-14 23:08:06] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-11-14 23:08:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:06] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-11-14 23:08:06] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2025-11-14 23:08:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:08:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-14 23:08:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:08:08] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:08:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:08:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:08:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-14 23:08:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-14 23:08:11] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2025-11-14 23:08:13] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-11-14 23:08:13] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:13] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-11-14 23:08:13] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-14 23:08:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:08:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:08:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:08:39] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-14 23:08:39] [TRACE] [OmnipathR] Downloaded 11 Kb in 25.836044s from omabrowser.org (436 bytes/s); Redirect: 0s, DNS look up: 0.001944s, Connection: 0.002669s, Pretransfer: 0.442029s, First byte at: 25.835928s
[2025-11-14 23:08:39] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 15 Nov 2025 04:08:39 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/tsv; charset=utf-8; content-length: 1187278; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2025-11-15_040837.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=8244793c6b91d491; expires=Mon, 15-Nov-2027 04:08:39 UTC; Path=/
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-11-14 23:08:42] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:42] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-11-14 23:08:42] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:42] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-11-14 23:08:42] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-11-14 23:08:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:08:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:08:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:08:43] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-14 23:08:43] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.918819s from rest.uniprot.org (33 bytes/s); Redirect: 0s, DNS look up: 0.018111s, Connection: 0.018927s, Pretransfer: 0.559316s, First byte at: 0.918741s
[2025-11-14 23:08:43] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 15 Nov 2025 04:08:43 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 15-October-2025
[2025-11-14 23:08:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-11-14 23:08:53] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-11-14 23:08:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:53] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-11-14 23:08:53] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-11-14 23:08:53] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] 13774 rows after translation; translated 13550 `uniprot_entry` IDs in column `id_organism_a` to 13550 `uniprot` IDs in column `id_organism_a`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-11-14 23:08:54] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:08:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:08:54] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-11-14 23:08:54] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:08:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:08:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:08:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:08:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-14 23:08:55] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.774306s from rest.uniprot.org (40 bytes/s); Redirect: 0s, DNS look up: 0.00191s, Connection: 0.00262s, Pretransfer: 0.47921s, First byte at: 0.774224s
[2025-11-14 23:08:55] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 15 Nov 2025 04:08:54 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 15-October-2025
[2025-11-14 23:09:01] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-11-14 23:09:01] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-11-14 23:09:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:01] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-11-14 23:09:01] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-11-14 23:09:01] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-14 23:09:01] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-14 23:09:01] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-14 23:09:01] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-11-14 23:09:01] [TRACE] [OmnipathR] 13774 rows after translation; translated 13253 `uniprot_entry` IDs in column `id_organism_b` to 13253 `uniprot` IDs in column `id_organism_b`.
[2025-11-14 23:09:02] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-11-14 23:09:02] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:02] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-11-14 23:09:02] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-14 23:09:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:09:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-14 23:09:02] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.533821s from rest.uniprot.org (80 bytes/s); Redirect: 0s, DNS look up: 0.001519s, Connection: 0.002388s, Pretransfer: 0.223861s, First byte at: 0.533759s
[2025-11-14 23:09:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 15 Nov 2025 04:09:02 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 15-October-2025
[2025-11-14 23:09:08] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-11-14 23:09:08] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-11-14 23:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:08] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-11-14 23:09:08] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] 163908 rows before translation, 12855 uniprot IDs in column `uniprot`.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] 163908 rows after translation; translated 12855 `uniprot` IDs in column `uniprot` to 12769 `genesymbol` IDs in column `genesymbol`.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:09:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:09:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:09:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:09:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.3645s from omnipathdb.org (43 Kb/s); Redirect: 0s, DNS look up: 0.001564s, Connection: 0.002306s, Pretransfer: 0.208737s, First byte at: 0.364153s
[2025-11-14 23:09:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:09:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:09:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:09:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:14] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:09:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-11-14 23:09:16] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-11-14 23:09:16] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-11-14 23:09:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:16] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-11-14 23:09:24] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Organism(s): 10090
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:09:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:09:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:09:35] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.361872s from omnipathdb.org (43.3 Kb/s); Redirect: 0s, DNS look up: 0.002001s, Connection: 0.002589s, Pretransfer: 0.207511s, First byte at: 0.361525s
[2025-11-14 23:09:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:09:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:09:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:09:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-11-14 23:09:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:40] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:09:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-11-14 23:09:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-11-14 23:09:41] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-11-14 23:09:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:09:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:09:41] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-11-14 23:09:48] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:09:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:09:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:09:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:09:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.573438s from omnipathdb.org (27.3 Kb/s); Redirect: 0s, DNS look up: 0.001473s, Connection: 0.002178s, Pretransfer: 0.407392s, First byte at: 0.572956s
[2025-11-14 23:09:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:09:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:09:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:10:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:10:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:02] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:10:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-14 23:10:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-14 23:10:02] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-11-14 23:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:02] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-11-14 23:10:04] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2025-11-14 23:10:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:10:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-14 23:10:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:10:04] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:10:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:10:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-14 23:10:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-14 23:10:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-14 23:10:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-14 23:10:06] [TRACE] [OmnipathR] Downloaded 9 Kb in 0.303123s from omnipathdb.org (29.8 Kb/s); Redirect: 0s, DNS look up: 0.001552s, Connection: 0.002223s, Pretransfer: 0.219691s, First byte at: 0.302743s
[2025-11-14 23:10:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 15 Nov 2025 04:10:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 15 Nov 2025 05:10:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-14 23:10:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:07] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-14 23:10:07] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-14 23:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:07] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-14 23:10:07] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-14 23:10:07] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:10:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-14 23:10:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-14 23:10:10] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2025-11-14 23:10:10] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-14 23:10:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-14 23:10:10] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-14 23:10:10] [TRACE] [OmnipathR] Orthology targets:
[2025-11-14 23:10:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-14 23:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-14 23:10:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-14 23:10:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-14 23:10:11] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-14 23:10:11] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-14 23:10:11] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-14 23:10:12] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
180.528 17.034 464.088
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.079 | 0.017 | 0.098 | |
| convert_f_defaults | 0.047 | 0.029 | 0.076 | |
| decouple | 0.001 | 0.000 | 0.000 | |
| dot-fit_preprocessing | 0.021 | 0.002 | 0.023 | |
| extract_sets | 0.022 | 0.000 | 0.022 | |
| filt_minsize | 0.036 | 0.005 | 0.041 | |
| get_collectri | 31.710 | 2.440 | 294.842 | |
| get_dorothea | 22.006 | 0.794 | 26.110 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 6.144 | 0.363 | 14.425 | |
| get_resource | 1.059 | 0.051 | 3.156 | |
| get_toy_data | 0.002 | 0.000 | 0.002 | |
| intersect_regulons | 0.029 | 0.003 | 0.032 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| rename_net | 0.038 | 0.003 | 0.041 | |
| run_aucell | 8.894 | 1.602 | 10.523 | |
| run_consensus | 1.999 | 0.240 | 2.239 | |
| run_fgsea | 21.614 | 0.527 | 22.148 | |
| run_gsva | 1.894 | 0.408 | 2.310 | |
| run_mdt | 0.137 | 0.026 | 0.162 | |
| run_mlm | 0.091 | 0.005 | 0.096 | |
| run_ora | 0.536 | 0.034 | 0.569 | |
| run_udt | 0.278 | 0.025 | 0.303 | |
| run_ulm | 0.074 | 0.009 | 0.083 | |
| run_viper | 0.970 | 0.189 | 1.163 | |
| run_wmean | 1.714 | 0.048 | 1.760 | |
| run_wsum | 0.732 | 0.090 | 0.821 | |
| show_methods | 0.044 | 0.016 | 0.059 | |
| show_resources | 0.180 | 0.025 | 0.961 | |
| tidyeval | 0 | 0 | 0 | |